Hi Daniel,
I must have missed your question regarding toolboxes in SPM, so maybe you already figured this out yourself. If you want to add a custom GUI for your toolbox, you will most likely want to have an entry for it in the SPM "Toolbox" pulldown in the main menu window. If you have computational modules that can be run within a batch job, you can add your toolbox there as well.
Both methods use some filename matching magic to make it easy to install new toolboxes without the need to change any SPM code or settings. In any case, your toolbox should live in its own folder below fullfile(spm('dir'),'toolbox'). To add your toolbox to the GUI pulldown, name your GUI startup file *_<yourToolboxName>.m, where <yourToolboxName> is the name of the folder you created. SPM will then create the pulldown menu entry and call your GUI startup file when the menu entry is selected. The batch system, on the other hand, will look for files names tbx_cfg_*.m and try to interpret them as batch GUI definition files.
Hope this helps,
Volkmar
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